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The Confederate was commissioned in the late 2260s as a prototype testbed for a new type of warp accelerator, a specially modified, energy-channeled dilithium crystal matrix installed where a Constitution-class vessel's dilithium crystal were normally activated.

On a test run in 2270, the Confederate attempted to run the warp drive through the accelerator matrix and ended up creating a warp in space that shot them towards the Romulan Star Empire. The crew was able to escape in the primary hull by initiating a saucer separation, but the secondary hull was not destroyed as expected, and was catapulted across the Romulan Neutral Zone. Starfleet Intelligence covered up all evidence of the dangerous warp accelerator tests following the accident. The creator of the warp accelerator, Virgil Brahms, was not even aware of the test, since after he concluded that the device was impractical, Starfleet had decided to test it anyway, without his knowledge.

The team, outfitted in surface operations blacksuniforms, left their shuttlecraft armed with phaser pistols and phaser rifles. After a running firefight, the crew made it to the Confederate, with only one casualty, Baskin. The team was able to restart the Confederate systems and lock the ship out from the Romulans influence, raising the deflector shield and leaving the depot. Several pursuit vessels fired on Confederate, causing damage, prompting Scott to energize the phasers for a Craig to order a futile warning shot and then initiating a warp speed jump away from the system. With systems failing, Craig began to key in the self destruct sequence for a suicide maneuver. Scott questioned the need for the effort, and put another plan into play. He signaled the Enterprise his intentions, to beam his team off of the ship while initiating a warp accelerator burt that would collapse subspace around the ship, damaging any pursuers that were not aware of the specific negative inverted plasma discharge required to nullify the effect. CaptainJames T. Kirk disobeyed Commodore Foley's order to let the suicide maneuver continue, just long enough to put Scotty's plan into play, discharging protective plasma, recovering the team and observing, from the Federation side of the Neutral Zone, as the Confederate disappeared into a spatial distortion. (TOS - Unlimitedcomic: "None But the Brave")

One hundred years later, Leah Brahms had taken an interest in her grandfather's writings regarding the warp accelerator, and had begun to research the tests on the Confederate, even though she did not have access to the classified records of the dramatic conclusion of the test, and the Confederate's loss. Brahms presented her theoretical findings about the possibilities of warp acceleration at the Theoretical Propulsion Group's biannual seminar at Starbase 313. Brahms and Geordi La Forge decided to run some practical tests on the warp acceleration theory by taking a runabout into open space, under the guise of a trip studying the Masa Cluster bound for Starbase 56. Before the pair could get started, they were captured by stowaway MajorRadak, a Romulan who had learned of Brahms's interest in the old experiment and had trailed her disguised as a Vulcanscientist. After bringing Brahms and La Forge aboard CommanderTomalak's D'Deridex-classwarbird, the Romulan plan was revealed. The Romulans had recently recovered the Confederate from the distortion and had again brought it to Cutuleh Minor. They wanted La Forge and Brahms to work on the warp accelerator so the Romulans could harness the power of the new propulsion system.

La Forge promptly used the warp drive on the Confederate to resonate in the pattern of his Starfleet serial number, alerting the USS Enterprise to his presence at the Romulan base. In an attempt to sabotage the Romulan plans, Brahms deactivated the magnetic field around the reactant injectors, triggering a buildup to a warp core breach. As the Romulans evacuated the base, the Enterprise-D beamed Brahms and La Forge to safety, moments before the antimatter went critical, destroying the Confederate and the Romulan base. (TNG - Unlimitedcomic: "Inheritance")